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Last change
on this file was
19708,
checked in by westram, 3 months ago
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- update doc+gui:
- avoid terms "ARB_NT" (=former name of main arb window), "ARB_NTREE" and similar
- instead talk about "ARB main window"
- correct refs to 'ARB/Probes/PT_SERVER Admin'.
- update 'What are marked species?'.
- update protection level documentation (parts already done with previous commit).
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-
Property svn:eol-style set to
native
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Property svn:keywords set to
Author Date Id Revision
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File size:
1.4 KB
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| 1 | # main topics: |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | |
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| 5 | # sub topics: |
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| 6 | #SUB subtopic.hlp |
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| 7 | |
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| 8 | # format described in ../help.readme |
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| 9 | |
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| 10 | |
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| 11 | TITLE Sort Tree Topology |
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| 12 | |
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| 13 | OCCURRENCE ARB/Tree/Beautify tree/... |
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| 14 | |
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| 15 | ARB_PARSIMONY/Tree/Beautify tree |
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| 16 | |
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| 17 | DESCRIPTION Arranges branches and groups according to the size of each |
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| 18 | subtree. If the size doesn't differ at a furcation, subtrees |
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| 19 | will be sorted alphabethically. This ensures the sorting is stable. |
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| 20 | |
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| 21 | Sorting does not change the tree topology, it only swaps branches! |
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| 22 | |
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| 23 | SECTION Available sort modes |
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| 24 | |
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| 25 | The first sort mode sorts the bigger branches to the top, |
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| 26 | the third sorts them to the bottom. |
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| 27 | |
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| 28 | The second sort mode sorts the bigger branches to the edges of the |
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| 29 | tree and the smaller branches to the center. |
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| 30 | |
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| 31 | The fourth and fifth mode are designed to sort the tree for |
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| 32 | the radial tree display mode. |
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| 33 | |
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| 34 | The fourth mode does the opposite of the second mode: it sorts |
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| 35 | bigger branches to the center and smaller ones to the borders |
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| 36 | of the tree. |
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| 37 | |
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| 38 | The fifth mode alternates between second and fourth mode. |
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| 39 | |
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| 40 | NOTES This facilitates the comparison of tree topologies resulting |
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| 41 | from different treeing approaches. |
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| 42 | |
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| 43 | See also LINK{resortbyother.hlp}. |
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| 44 | |
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| 45 | In ARB_PARSIMONY you cannot select the beautification method: it will |
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| 46 | always sort bigger branches to top. This will also happen automatically |
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| 47 | after LINK{pa_optimizer.hlp}. |
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| 48 | |
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| 49 | EXAMPLES None |
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| 50 | |
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| 51 | WARNINGS None |
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| 52 | |
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| 53 | BUGS No bugs known |
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